Data from: Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in slipper orchid genus Cypripedium L.

Background and Aims: Cypripedium is the most widespread and
morphologically diverse genus of slipper orchids. Despite several
published phylogenies, the topology and monophyly of its infrageneric taxa
remained uncertain. Here, we aimed to reconstruct a robust section-level
phylogeny of Cypripedium and explore its evolutionary history using target
capture data for the first time. Methods:  We used the
orchid-specific bait set Orchidaceae963 in combination with transcriptomic
data to reconstruct the phylogeny of Cypripedium based on 913 nuclear
loci, covering all 13 sections. Subsequently, we investigated discordance
among nuclear and chloroplast trees, estimated divergence times and
ancestral ranges, searched for anomaly zones, polytomies, and
diversification rate shifts, and identified potential gene (genome)
duplication and hybridization events. Key Results: All sections
were recovered as monophyletic, contrary to the two subsections within
sect. Cypripedium. The two subclades within this section did not
correspond to its subsections but matched the geographic distribution of
their species. Additionally, we discovered high levels of discordance in
the short backbone branches of the genus and within sect. Cypripedium,
which can be attributed to hybridization events detected based on
phylogenetic network analyses, and incomplete lineage sorting caused by
rapid radiation. Our biogeographic analysis suggested a Neotropical origin
of the genus during the Oligocene (~30 Ma), with a lineage of potentially
hybrid origin spreading to the Old World in the Early Miocene (~22 Ma).
The rapid radiation at the backbone likely occurred in Southeast Asia
around the Middle Miocene Climatic Transition (~15–13 Ma), followed by
several independent dispersals back to the New World. Moreover, the
Pliocene-Quaternary glacial cycles may have contributed to further
speciation and reticulate evolution within Cypripedium.
Conclusions: Our study provided novel insights into the
evolutionary history of Cypripedium based on high-throughput molecular
data, shedding light on the dynamics of its distribution and diversity
patterns from its origin to the present.